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QuaC stalls [when creating singularity+conda environments](https://gitlab.rc.uab.edu/center-for-computational-genomics-and-data-science/sciops/pipelines/quac#create-singularityconda-environments-for-t…
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In GitLab by @deeptha on Jul 23, 2021, 16:25
_Merges rc_scripts -> master_
I created scripts for recommended and required functions and aliases, `.requiredcrc` and `.recommendedrc`.
Things to chec…
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Using samtools version 1.13, I am getting an unexpected odd value in count of paired reads in metrics (DUPLICATE PAIR OPTICAL).
#### Are you using the latest version of [samtools](https://github…
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**User story**
As representative for SSR (Rich C) we would like to be able to pint plate and tube labels on the new Squix printers from SS as the Toshiba TEC are increasing unreliable.
**Who are t…
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Copied from: https://gitlab.rc.uab.edu/center-for-computational-genomics-and-data-science/sciops/pipelines/small_variant_caller_pipeline/-/issues/42
A fun one to be sure. Recently a few runs of the p…
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samtools ampliconstats doesn't support multi reference sequence/contig genomes (known issue) but it would be really nice if could or if the lack of support was clearly documented and handled cleanly b…
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In GitLab by @ManavalanG on Mar 16, 2021, 23:06
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_Merges vep_annotation -> master_
Annotates variants in VCF using Variant Effect Predictor (VEP).
The following may need review at some level. Note this other stuff may need review as well, as this …
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**Is your feature request related to a problem? Please describe.**
As discussed in https://github.com/MillionConcepts/pdr/issues/12 there are some PDS3 products which are technically invalid, but for…
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In GitLab by @wilkb777 on Jan 31, 2021, 15:38
_Merges vep_output_parsing -> master_
A simple, no frills, parser for taking VEP annotated VCFs and parsing them into a TSV format for easier downstream…